With Dana safe at the hospital, Alex Mercer resumes his hunt. As instructed by Dr. Ragland, Alex attends the phone call at one of the booths. The caller implies that Mercer's body hosts the Blacklight virus, that he's now no longer a human being. He informs Mercer that the virus had taken over his body when he was killed at Penn station. The caller suggests Mercer to visit Blackwatch's command post for further evidence.

Alex infiltrates one of Blackwatch's extraction units and extracts multiple other ground units. Eventually, Mercer's unit is called back to a debriefing and he uses this opportunity to get inside the base, as suggested by the mysterious caller.

As Alex enters the facility, Blackwatch soldiers are being debriefed about Bloodtox deployment. The commander details that Bloodtox only affected individuals infected with the virus and it was completely inert to human beings. However, the chemical was being pumped into the room with soldiers. Alex is suffocated, and tries to escape from the base. However, he is confronted by D-code soldiers, Blackwatch's new elite soldiers created specifically to fight Mercer. He eliminates this new foe along with the regular military forces and escapes the base.

With confirmation of Bloodtox's effect on Mercer, Blackwatch prepares for a city wide deployment.